P. Hohenberg and W. Kohn, Inhomogeneous Electron Gas, Physical Review, vol.136, issue.3B, pp.B864-B871, 1964.

R. G. Parr and W. Yang, Density-Functional Theory of Atoms and Molecules, 1989.

E. K. Gross, C. A. Ullrich, and U. J. Gossmann, Density Functional Theory of Time-Dependent Systems, NATO ASI Series, pp.149-171, 1995.

A. Savin, On degeneracy, near-degeneracy and density functional theory, Theoretical and Computational Chemistry, pp.327-357, 1996.

W. Kohn and L. J. Sham, Self-Consistent Equations Including Exchange and Correlation Effects, Physical Review, vol.140, issue.4A, pp.A1133-A1138, 1965.

A. D. Becke, Perspective: Fifty years of density-functional theory in chemical physics, The Journal of Chemical Physics, vol.140, issue.18, p.18A301, 2014.

N. Mardirossian and M. Head-gordon, Thirty years of density functional theory in computational chemistry: an overview and extensive assessment of 200 density functionals, Molecular Physics, vol.115, issue.19, pp.2315-2372, 2017.

J. Neugebauer and T. Hickel, Density functional theory in materials science, Wiley Interdisciplinary Reviews: Computational Molecular Science, vol.3, issue.5, pp.438-448, 2013.

T. Bally and G. N. Sastry, Incorrect Dissociation Behavior of Radical Ions in Density Functional Calculations, The Journal of Physical Chemistry A, vol.101, issue.43, pp.7923-7925, 1997.

J. Gräfenstein, E. Kraka, and D. Cremer, The impact of the self-interaction error on the density functional theory description of dissociating radical cations: Ionic and covalent dissociation limits, The Journal of Chemical Physics, vol.120, issue.2, pp.524-539, 2004.

J. Gräfenstein, E. Kraka, and D. Cremer, Effect of the self-interaction error for three-electron bonds: On the development of new exchange-correlation functionals, Phys. Chem. Chem. Phys., vol.6, issue.6, pp.1096-1112, 2004.

J. Gräfenstein and D. Cremer, The self-interaction error and the description of non-dynamic electron correlation in density functional theory, Theoretical Chemistry Accounts, vol.123, issue.3-4, pp.171-182, 2009.

J. L. Bao, L. Gagliardi, and D. G. Truhlar, Self-Interaction Error in Density Functional Theory: An Appraisal, The Journal of Physical Chemistry Letters, vol.9, issue.9, pp.2353-2358, 2018.

T. Leininger, H. Stoll, H. Werner, and A. Savin, Combining long-range configuration interaction with short-range density functionals, Chemical Physics Letters, vol.275, issue.3-4, pp.151-160, 1997.

E. Goll, H. Werner, and H. Stoll, A short-range gradient-corrected density functional in long-range coupled-cluster calculations for rare gas dimers, Physical Chemistry Chemical Physics, vol.7, issue.23, p.3917, 2005.

E. Goll, H. J. Werner, and H. Stoll, Short-range density functionals in combination with local long-range ab initio methods: Application to non-bonded complexes, Chemical Physics, vol.346, issue.1-3, pp.257-265, 2008.

J. Toulouse, F. Colonna, and A. Savin, Long-range?short-range separation of the electron-electron interaction in density-functional theory, Physical Review A, vol.70, issue.6, p.62505, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00981846

D. Porezag, T. H. Frauenheim, T. H. Köhler, G. Seifert, and R. Kaschner, Construction of tight-binding-like potentials on the basis of density-functional theory: Application to carbon, Physical Review B, vol.51, issue.19, pp.12947-12957, 1995.

G. Seifert, D. Porezag, and T. H. Frauenheim, Calculations of molecules, clusters, and solids with a simplified LCAO-DFT-LDA scheme, International Journal of Quantum Chemistry, vol.58, issue.2, pp.185-192, 1996.

M. Elstner, D. Porezag, G. Jungnickel, J. Elsner, M. Haugk et al., Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties, Physical Review B, vol.58, issue.11, pp.7260-7268, 1998.

E. H. Hückel, Miscellany, New England Journal of Medicine, vol.204, issue.2, pp.85-86, 1931.

M. Wolfsberg and L. Helmholz, The Spectra and Electronic Structure of the Tetrahedral Ions MnO4?, CrO4??, and ClO4?, The Journal of Chemical Physics, vol.20, issue.5, pp.837-843, 1952.

R. Hoffmann, An Extended Hückel Theory. I. Hydrocarbons, The Journal of Chemical Physics, vol.39, issue.6, pp.1397-1412, 1963.

R. Hoffmann, Extended Hückel Theory. III. Compounds of Boron and Nitrogen, The Journal of Chemical Physics, vol.40, issue.9, pp.2474-2480, 1964.

R. Hoffmann, Extended hückel theory?v, Tetrahedron, vol.22, issue.2, pp.521-538, 1966.

D. J. Chadi, (110) surface atomic structures of covalent and ionic semiconductors, Physical Review B, vol.19, issue.4, pp.2074-2082, 1979.

W. A. Harrison, Electronic structure and the properties of solids, 1980.

J. Friedel, The physics of metals, J. M. Ziman, 1969.

M. C. Desjonquères and D. Spanjaard, Concepts in Surface Physics, Concepts in Surface Physics, vol.30, 1993.

C. Noguera, INSULATING OXIDES IN LOW DIMENSIONALITY: A THEORETICAL REVIEW, Surface Review and Letters, vol.08, issue.01n02, pp.121-167, 2001.
URL : https://hal.archives-ouvertes.fr/hal-00002630

J. A. Pople, D. P. Santry, and G. A. Segal, Approximate Self?Consistent Molecular Orbital Theory. I. Invariant Procedures, The Journal of Chemical Physics, vol.43, issue.10, pp.S129-S135, 1965.

M. J. Dewar and W. Thiel, Ground states of molecules. 38. The MNDO method. Approximations and parameters, Journal of the American Chemical Society, vol.99, issue.15, pp.4899-4907, 1977.

M. J. Dewar, E. G. Zoebisch, E. F. Healy, and J. J. Stewart, Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model, Journal of the American Chemical Society, vol.107, issue.13, pp.3902-3909, 1985.

J. J. Stewart, Optimization of parameters for semiempirical methods I. Method, Journal of Computational Chemistry, vol.10, issue.2, pp.209-220, 1989.

C. M. Goringe, D. R. Bowler, and E. Hernández, Tight-binding modelling of materials, Reports on Progress in Physics, vol.60, issue.12, pp.1447-1512, 1997.

T. Frauenheim, G. Seifert, M. Elstner, T. Niehaus, C. Köhler et al., Atomistic simulations of complex materials: ground-state and excited-state properties, Journal of Physics: Condensed Matter, vol.14, issue.11, pp.3015-3047, 2002.

J. C. Slater and G. F. Koster, Simplified LCAO Method for the Periodic Potential Problem, Physical Review, vol.94, issue.6, pp.1498-1524, 1954.

J. A. Majewski and P. Vogl, Simple model for structural properties and crystal stability ofsp-bonded solids, Physical Review B, vol.35, issue.18, pp.9666-9682, 1987.

M. Kohyama, R. Yamamoto, Y. Ebata, and M. Kinoshita, Atomic forces in the self-consistent tight-binding model, physica status solidi (b), vol.152, issue.2, pp.533-541, 1989.

F. Liu, Self-consistent tight-binding method, Physical Review B, vol.52, issue.15, pp.10677-10680, 1995.

O. F. Sankey and D. J. Niklewski, Ab initiomulticenter tight-binding model for molecular-dynamics simulations and other applications in covalent systems, Physical Review B, vol.40, issue.6, pp.3979-3995, 1989.

M. S. Tang, C. Z. Wang, C. T. Chan, and K. M. Ho, Environment-dependent tight-binding potential model, Physical Review B, vol.53, issue.3, pp.979-982, 1996.

A. P. Horsfield and A. M. Bratkovsky, Ab initiotight binding, Journal of Physics: Condensed Matter, vol.12, issue.2, pp.R1-R24, 1999.

Z. M. Khakimov, P. L. Tereshchuk, N. T. Sulaymanov, F. T. Umarova, and M. T. Swihart, Nonconventional tight-binding method for the calculation of the total energy and spectroscopic energies of atomic clusters: Transferable parameters for silicon, Physical Review B, vol.72, issue.11, pp.115335-115346, 2005.

C. Leahy, M. Yu, C. S. Jayanthi, and S. Y. Wu, Coherent treatment of the self-consistency and the environment-dependency in a semi-empirical Hamiltonian: Applications to bulk silicon, silicon surfaces, and silicon clusters, Physical Review B, vol.74, issue.15, pp.155408-155421, 2006.

D. A. Areshkin, O. A. Shenderova, J. D. Schall, S. P. Adiga, and D. W. Brenner, A self-consistent tight binding model for hydrocarbon systems: application to quantum transport simulation, Journal of Physics: Condensed Matter, vol.16, issue.39, pp.6851-6866, 2004.

A. Zlobin, Y. Mokrushina, S. Terekhov, A. Zalevsky, T. Bobik et al., QM/MM Description of Newly Selected Catalytic Bioscavengers Against Organophosphorus Compounds Revealed Reactivation Stimulus Mediated by Histidine Residue in the Acyl-Binding Loop, Frontiers in Pharmacology, vol.9, p.834, 2018.

R. S. Mulliken, Electronic Population Analysis on LCAO?MO Molecular Wave Functions. I, The Journal of Chemical Physics, vol.23, issue.10, pp.1833-1840, 1955.

S. Kaminski, T. J. Giese, M. Gaus, D. M. York, and M. Elstner, Extended Polarization in Third-Order SCC-DFTB from Chemical-Potential Equalization, The Journal of Physical Chemistry A, vol.116, issue.36, pp.9131-9141, 2012.

S. G. Srinivasan, N. Goldman, I. Tamblyn, S. Hamel, and M. Gaus, A Density Functional Tight Binding Model with an Extended Basis Set and Three-Body Repulsion for Hydrogen under Extreme Thermodynamic Conditions, The Journal of Physical Chemistry A, vol.118, issue.29, pp.5520-5528, 2014.

. Yang, H. Yu, D. York, Q. Cui, and M. Elstner, Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method: Third-Order Expansion of the Density Functional Theory Total Energy and Introduction of a Modified Effective Coulomb Interaction, The Journal of Physical Chemistry A, vol.111, issue.42, pp.10861-10873, 2007.

M. Wahiduzzaman, A. F. Oliveira, P. Philipsen, L. Zhechkov, E. Van-lenthe et al., DFTB Parameters for the Periodic Table: Part 1, Electronic Structure, Journal of Chemical Theory and Computation, vol.9, issue.9, pp.4006-4017, 2013.

A. F. Oliveira, P. Philipsen, and T. Heine, DFTB Parameters for the Periodic Table, Part 2: Energies and Energy Gradients from Hydrogen to Calcium, Journal of Chemical Theory and Computation, vol.11, issue.11, pp.5209-5218, 2015.

M. Gaus, C. Chou, H. Witek, and M. Elstner, Automatized Parametrization of SCC-DFTB Repulsive Potentials: Application to Hydrocarbons?, The Journal of Physical Chemistry A, vol.113, issue.43, pp.11866-11881, 2009.

C. Chou, Y. Nishimura, C. Fan, G. Mazur, S. Irle et al., Automatized Parameterization of DFTB Using Particle Swarm Optimization, Journal of Chemical Theory and Computation, vol.12, issue.1, pp.53-64, 2015.

Z. Bodrog, B. Aradi, and T. Frauenheim, Automated Repulsive Parametrization for the DFTB Method, Journal of Chemical Theory and Computation, vol.7, issue.8, pp.2654-2664, 2011.

M. P. Lourenço, M. C. Da-silva, A. F. Oliveira, M. C. Quintão, and H. A. Duarte, FASP: a framework for automation of Slater?Koster file parameterization, Theoretical Chemistry Accounts, vol.135, issue.11, p.250, 2016.

M. Doemer, E. Liberatore, J. M. Knaup, I. Tavernelli, and U. Rothlisberger, In situparameterisation of SCC-DFTB repulsive potentials by iterative Boltzmann inversion, Molecular Physics, vol.111, issue.22-23, pp.3595-3607, 2013.

M. Van-den-bossche, DFTB-Assisted Global Structure Optimization of 13- and 55-Atom Late Transition Metal Clusters, The Journal of Physical Chemistry A, vol.123, issue.13, pp.3038-3045, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02181710

J. J. Kranz, M. Kubillus, R. Ramakrishnan, O. A. Von-lilienfeld, and M. Elstner, Generalized Density-Functional Tight-Binding Repulsive Potentials from Unsupervised Machine Learning, Journal of Chemical Theory and Computation, vol.14, issue.5, pp.2341-2352, 2018.

J. Frenzel, A. F. Oliveira, N. Jardillier, T. Heine, and G. Seifert, Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) Parameters for Ceria in 0D to 3D

M. Gaus, A. Goez, and M. Elstner, Parametrization and Benchmark of DFTB3 for Organic Molecules, Journal of Chemical Theory and Computation, vol.9, issue.1, pp.338-354, 2012.

C. Köhler, Z. Hajnal, P. Deák, T. Frauenheim, and S. Suhai, Theoretical investigation of carbon defects and diffusion in ?-quartz, Physical Review B, vol.64, issue.8, p.85333, 2001.

T. J. Giese and D. M. York, Density-functional expansion methods: grand challenges, Theoretical Chemistry Accounts, vol.131, issue.3, p.1145, 2012.

A. S. Christensen, M. Elstner, and Q. Cui, Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization, The Journal of Chemical Physics, vol.143, issue.8, p.084123, 2015.

C. Iftner, A. Simon, K. Korchagina, M. Rapacioli, and F. Spiegelman, A density functional tight binding/force field approach to the interaction of molecules with rare gas clusters: Application to (C6H6)+/0Arn clusters, The Journal of Chemical Physics, vol.140, issue.3, p.034301, 2014.

Y. Zhao and D. G. Truhlar, The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals, Theoretical Chemistry Accounts, vol.120, issue.1-3, pp.215-241, 2007.

M. Dion, H. Rydberg, E. Schröder, D. C. Langreth, and B. I. Lundqvist, Erratum: Van der Waals Density Functional for General Geometries [Phys. Rev. Lett.92, 246401 (2004)], Physical Review Letters, vol.95, issue.10, pp.246401-246405, 2005.

T. Sato, T. Tsuneda, and K. Hirao, Long-range corrected density functional study on weakly bound systems: Balanced descriptions of various types of molecular interactions, The Journal of Chemical Physics, vol.126, issue.23, p.234114, 2007.

D. C. Langreth, M. Dion, H. Rydberg, E. Schröder, P. Hyldgaard et al., Van der Waals density functional theory with applications, International Journal of Quantum Chemistry, vol.101, issue.5, pp.599-610, 2004.

S. D. Chakarova-käck, E. Schröder, B. I. Lundqvist, and D. C. Langreth, Application of van der Waals Density Functional to an Extended System: Adsorption of Benzene and Naphthalene on Graphite, Physical Review Letters, vol.96, issue.14, pp.146107-146111, 2006.

T. Thonhauser, V. R. Cooper, S. Li, A. Puzder, P. Hyldgaard et al., Van der Waals density functional: Self-consistent potential and the nature of the van der Waals bond, Physical Review B, vol.76, issue.12, pp.125112-125123, 2007.

O. A. Von-lilienfeld, I. Tavernelli, U. Rothlisberger, and D. Sebastiani, Optimization of Effective Atom Centered Potentials for London Dispersion Forces in Density Functional Theory, Physical Review Letters, vol.93, issue.15, pp.153004-153008, 2004.

J. Gräfenstein and D. Cremer, An efficient algorithm for the density-functional theory treatment of dispersion interactions, The Journal of Chemical Physics, vol.130, issue.12, p.124105, 2009.

J. P. Lewis and O. F. Sankey, Geometry and energetics of DNA basepairs and triplets from first principles quantum molecular relaxations, Biophysical Journal, vol.69, issue.3, pp.1068-1076, 1995.

E. J. Meijer and M. Sprik, A density?functional study of the intermolecular interactions of benzene, The Journal of Chemical Physics, vol.105, issue.19, pp.8684-8689, 1996.

F. A. Gianturco, F. Paesani, M. F. Laranjeira, V. Vassilenko, and M. A. Cunha, Intermolecular forces from density functional theory. III. A multiproperty analysis for the Ar(1S)-CO(1?) interaction, The Journal of Chemical Physics, vol.110, issue.16, pp.7832-7845, 1999.

Q. Wu and W. Yang, Empirical correction to density functional theory for van der Waals interactions, The Journal of Chemical Physics, vol.116, issue.2, pp.515-524, 2002.

U. Zimmerli, M. Parrinello, and P. Koumoutsakos, Dispersion corrections to density functionals for water aromatic interactions, The Journal of Chemical Physics, vol.120, issue.6, pp.2693-2699, 2004.

A. Goursot, T. Mineva, R. Kevorkyants, and D. Talbi, Interaction between n-Alkane Chains: Applicability of the Empirically Corrected Density Functional Theory for Van der Waals Complexes, Journal of Chemical Theory and Computation, vol.3, issue.3, pp.755-763, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00340277

S. Grimme, Accurate description of van der Waals complexes by density functional theory including empirical corrections, Journal of Computational Chemistry, vol.25, issue.12, pp.1463-1473, 2004.

M. Elstner, The SCC-DFTB method and its application to biological systems, Theoretical Chemistry Accounts, vol.116, issue.1-3, pp.316-325, 2005.

L. Zhechkov, T. Heine, S. Patchkovskii, G. Seifert, and H. A. Duarte, An Efficienta PosterioriTreatment for Dispersion Interaction in Density-Functional-Based Tight Binding, Journal of Chemical Theory and Computation, vol.1, issue.5, pp.841-847, 2005.

M. Rapacioli, F. Spiegelman, D. Talbi, T. Mineva, A. Goursot et al., Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: Application to polycyclic aromatic hydrocarbon clusters, The Journal of Chemical Physics, vol.130, issue.24, p.244304, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00418594

S. Grimme, Semiempirical GGA-type density functional constructed with a long-range dispersion correction, Journal of Computational Chemistry, vol.27, issue.15, pp.1787-1799, 2006.

S. Grimme, J. Antony, S. Ehrlich, and H. Krieg, A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu, The Journal of Chemical Physics, vol.132, issue.15, p.154104, 2010.

R. F. Bader, The Lagrangian Approach to Chemistry, The Quantum Theory of Atoms in Molecules, pp.35-59

P. Lowdin, On the Non?Orthogonality Problem Connected with the Use of Atomic Wave Functions in the Theory of Molecules and Crystals, The Journal of Chemical Physics, vol.18, issue.3, pp.365-375, 1950.

J. Li, T. Zhu, C. J. Cramer, and D. G. Truhlar, New Class IV Charge Model for Extracting Accurate Partial Charges from Wave Functions, The Journal of Physical Chemistry A, vol.102, issue.10, pp.1820-1831, 1998.

I. Mayer, Charge, bond order and valence in the AB initio SCF theory, Chemical Physics Letters, vol.97, issue.3, pp.270-274, 1983.

J. A. Kalinowski, B. Lesyng, J. D. Thompson, C. J. Cramer, and D. G. Truhlar, Class IV Charge Model for the Self-Consistent Charge Density-Functional Tight-Binding Method, The Journal of Physical Chemistry A, vol.108, issue.13, pp.2545-2549, 2004.

E. Michoulier, N. Ben-amor, M. Rapacioli, J. A. Noble, J. Mascetti et al., Theoretical determination of adsorption and ionisation energies of polycyclic aromatic hydrocarbons on water ice, Physical Chemistry Chemical Physics, vol.20, issue.17, pp.11941-11953, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01764650

Y. Wu, A. Ilie, and S. Crampin, Self-consistent charge and dipole density functional tight binding method and application to carbon-based systems, Computational Materials Science, vol.134, pp.206-213, 2017.

C. Köhler, G. Seifert, U. Gerstmann, M. Elstner, H. Overhof et al., Approximate density-functional calculations of spin densities in large molecular systems and complex solids, Physical Chemistry Chemical Physics, vol.3, issue.23, pp.5109-5114, 2001.

C. Köhler, T. Frauenheim, B. Hourahine, G. Seifert, and M. Sternberg, Treatment of Collinear and Noncollinear Electron Spin within an Approximate Density Functional Based Method?, The Journal of Physical Chemistry A, vol.111, issue.26, pp.5622-5629, 2007.

J. F. Janak, Proof that?E?ni=?in density-functional theory, Physical Review B, vol.18, issue.12, pp.7165-7168, 1978.

P. Melix, A. F. Oliveira, R. Rüger, and T. Heine, Spin polarization in SCC-DFTB, Theoretical Chemistry Accounts, vol.135, issue.9, p.232, 2016.

P. Mori-sánchez, A. J. Cohen, and W. Yang, Many-electron self-interaction error in approximate density functionals, The Journal of Chemical Physics, vol.125, issue.20, p.201102, 2006.

J. P. Perdew and A. Zunger, Self-interaction correction to density-functional approximations for many-electron systems, Physical Review B, vol.23, issue.10, pp.5048-5079, 1981.

F. Aryasetiawan and O. Gunnarsson, TheGWmethod, Reports on Progress in Physics, vol.61, issue.3, pp.237-312, 1998.

P. R. I.-de, F. Moreira, R. L. Illas, and . Martin, Phys. Rev. B, p.155102, 2002.

V. I. Anisimov, F. Aryasetiawan, and A. I. Lichtenstein, First-principles calculations of the electronic structure and spectra of strongly correlated systems: theLDA+Umethod, Journal of Physics: Condensed Matter, vol.9, issue.4, pp.767-808, 1997.

D. Vogel, P. Krüger, and J. Pollmann, Self-interaction and relaxation-corrected pseudopotentials for II-VI semiconductors, Physical Review B, vol.54, issue.8, pp.5495-5511, 1996.

D. Vogel, P. Krüger, and J. Pollmann, Ab initioelectronic structure of silver halides calculated with self-interaction and relaxation-corrected pseudopotentials, Physical Review B, vol.58, issue.7, pp.3865-3869, 1998.

A. Filippetti and N. A. Spaldin, Strong-correlation effects in Born effective charges, Physical Review B, vol.68, issue.4, p.125109, 2003.

B. Hourahine, S. Sanna, B. Aradi, C. Köhler, T. H. Niehaus et al., Self-Interaction and Strong Correlation in DFTB?, The Journal of Physical Chemistry A, vol.111, issue.26, pp.5671-5677, 2007.

T. Van-voorhis, T. Kowalczyk, B. Kaduk, L. Wang, C. Cheng et al., The Diabatic Picture of Electron Transfer, Reaction Barriers, and Molecular Dynamics, Annual Review of Physical Chemistry, vol.61, issue.1, pp.149-170, 2010.

A. De-la-lande and D. R. Salahub, Derivation of interpretative models for long range electron transfer from constrained density functional theory, Journal of Molecular Structure: THEOCHEM, vol.943, issue.1-3, pp.115-120, 2010.

T. Kuba?, P. B. Woiczikowski, G. Cuniberti, and M. Elstner, J. Phys. Chem. B, vol.112, pp.7937-7947, 2008.

T. Kuba? and M. Elstner, J. Phys. Chem. B, vol.112, pp.8788-8798, 2008.

T. Kuba?, U. Kleinekathöfer, and M. Elstner, J. Phys. Chem. B, vol.113, pp.13107-13117, 2009.

P. B. Woiczikowski, T. Kuba?, R. Gutiérrez, R. A. Caetano, G. Cuniberti et al., Combined density functional theory and Landauer approach for hole transfer in DNA along classical molecular dynamics trajectories, The Journal of Chemical Physics, vol.130, issue.21, p.215104, 2009.

R. G. Endres, D. L. Cox, and R. R. Singh, Colloquium: The quest for high-conductance DNA, Reviews of Modern Physics, vol.76, issue.1, pp.195-214, 2004.

K. Senthilkumar, F. C. Grozema, C. F. Guerra, F. M. Bickelhaupt, F. D. Lewis et al., Absolute Rates of Hole Transfer in DNA, Journal of the American Chemical Society, vol.127, issue.42, pp.14894-14903, 2005.

T. Kuba? and M. Elstner, J. Phys. Chem. B, vol.114, pp.11221-11240, 2010.

Q. Wu and T. Van-voorhis, Direct optimization method to study constrained systems within density-functional theory, Physical Review A, vol.72, issue.2, pp.24502-24506, 2005.

Q. Wu and T. Van-voorhis, Direct Calculation of Electron Transfer Parameters through Constrained Density Functional Theory, The Journal of Physical Chemistry A, vol.110, issue.29, pp.9212-9218, 2006.

Q. Wu and T. Van-voorhis, Constrained Density Functional Theory and Its Application in Long-Range Electron Transfer, Journal of Chemical Theory and Computation, vol.2, issue.3, pp.765-774, 2006.

Q. Wu and T. Van-voorhis, Extracting electron transfer coupling elements from constrained density functional theory, The Journal of Chemical Physics, vol.125, issue.16, p.164105, 2006.

Q. Wu, C. Cheng, and T. Van-voorhis, Configuration interaction based on constrained density functional theory: A multireference method, The Journal of Chemical Physics, vol.127, issue.16, p.164119, 2007.

M. Rapacioli and F. Spiegelman, Modelling singly ionized coronene clusters, The European Physical Journal D, vol.52, issue.1-3, pp.55-58, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00844588

M. Rapacioli, F. Spiegelman, A. Scemama, and A. Mirtschink, Modeling Charge Resonance in Cationic Molecular Clusters: Combining DFT-Tight Binding with Configuration Interaction, Journal of Chemical Theory and Computation, vol.7, issue.1, pp.44-55, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00844617

V. Lutsker, B. Aradi, and T. A. Niehaus, Implementation and benchmark of a long-range corrected functional in the density functional based tight-binding method, The Journal of Chemical Physics, vol.143, issue.18, p.184107, 2015.

Q. Cui, M. Elstner, E. Kaxiras, T. Frauenheim, and M. Karplus, A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method, The Journal of Physical Chemistry B, vol.105, issue.2, pp.569-585, 2001.

G. D. Seabra, R. C. Walker, M. Elstner, D. A. Case, and A. E. Roitberg, Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package?, The Journal of Physical Chemistry A, vol.111, issue.26, pp.5655-5664, 2007.

T. Kuba?, K. Welke, and G. Groenhof, New QM/MM implementation of the DFTB3 method in the gromacs package, Journal of Computational Chemistry, vol.36, issue.26, pp.1978-1989, 2015.

A. Simon, J. A. Noble, G. Rouaut, A. Moudens, C. Aupetit et al., Formation of coronene:water complexes: FTIR study in argon matrices and theoretical characterisation, Physical Chemistry Chemical Physics, vol.19, issue.12, pp.8516-8529, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01494011

M. Lundberg, Y. Sasakura, G. Zheng, and K. Morokuma, Case Studies of ONIOM(DFT:DFTB) and ONIOM(DFT:DFTB:MM) for Enzymes and Enzyme Mimics, Journal of Chemical Theory and Computation, vol.6, issue.4, pp.1413-1427, 2010.

Y. Nishimoto, DFTB/PCM Applied to Ground and Excited State Potential Energy Surfaces, The Journal of Physical Chemistry A, vol.120, issue.5, pp.771-784, 2016.

T. A. Niehaus, S. Suhai, F. Della-sala, P. Lugli, M. Elstner et al., Tight-binding approach to time-dependent density-functional response theory, Physical Review B, vol.63, issue.8, p.85108, 2001.

M. E. Casida, Time-Dependent Density Functional Response Theory for Molecules, Recent Advances in Density Functional Methods, pp.155-192, 1995.

M. E. Casida, Time-dependent density-functional theory for molecules and molecular solids, Journal of Molecular Structure: THEOCHEM, vol.914, issue.1-3, pp.3-18, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01659057

R. Rüger, T. Niehaus, E. Van-lenthe, T. Heine, and L. Visscher, Vibrationally resolved UV/Vis spectroscopy with time-dependent density functional based tight binding, The Journal of Chemical Physics, vol.145, issue.18, p.184102, 2016.

F. Trani, G. Scalmani, G. Zheng, I. Carnimeo, M. J. Frisch et al., Time-Dependent Density Functional Tight Binding: New Formulation and Benchmark of Excited States, Journal of Chemical Theory and Computation, vol.7, issue.10, pp.3304-3313, 2011.

A. Domínguez, B. Aradi, T. Frauenheim, V. Lutsker, and T. A. Niehaus, Extensions of the Time-Dependent Density Functional Based Tight-Binding Approach, Journal of Chemical Theory and Computation, vol.9, issue.11, pp.4901-4914, 2013.

A. Humeniuk and R. Mitri?, Long-range correction for tight-binding TD-DFT, The Journal of Chemical Physics, vol.143, issue.13, p.134120, 2015.

J. J. Kranz, M. Elstner, B. Aradi, T. Frauenheim, V. Lutsker et al., Time-Dependent Extension of the Long-Range Corrected Density Functional Based Tight-Binding Method, Journal of Chemical Theory and Computation, vol.13, issue.4, pp.1737-1747, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02289045

R. Chen, A. J. Aquino, N. H. Sue, T. Niehaus, and H. Lischka, Characterization of Charge Transfer in Excited States of Extended Clusters of ?-Stacked Donor and Acceptor Complexes in Lock-Arm Supramolecular Ordering, The Journal of Physical Chemistry A, vol.123, issue.21, pp.4532-4542, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02364832

X. Gao, S. Bai, D. Fazzi, T. Niehaus, M. Barbatti et al., Evaluation of Spin-Orbit Couplings with Linear-Response Time-Dependent Density Functional Methods, Journal of Chemical Theory and Computation, vol.13, issue.2, pp.515-524, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02288755

R. Rüger, E. Van-lenthe, Y. Lu, J. Frenzel, T. Heine et al., Efficient Calculation of Electronic Absorption Spectra by Means of Intensity-Selected Time-Dependent Density Functional Tight Binding, Journal of Chemical Theory and Computation, vol.11, issue.1, pp.157-167, 2014.

T. Niehaus, Approximate time-dependent density functional theory, Journal of Molecular Structure: THEOCHEM, vol.914, issue.1-3, pp.38-49, 2009.

P. Plötz, T. Niehaus, and O. Kühn, A new efficient method for calculation of Frenkel exciton parameters in molecular aggregates, The Journal of Chemical Physics, vol.140, issue.17, p.174101, 2014.

P. Plötz, J. Megow, T. Niehaus, and O. Kühn, Spectral densities for Frenkel exciton dynamics in molecular crystals: A TD-DFTB approach, The Journal of Chemical Physics, vol.146, issue.8, p.084112, 2017.

J. Freitag, A. Domínguez, T. A. Niehaus, A. Hülsewig, R. Dillert et al., Nitrogen(II) Oxide Charge Transfer Complexes on TiO2: A New Source for Visible-Light Activity, The Journal of Physical Chemistry C, vol.119, issue.9, pp.4488-4501, 2015.

L. Dontot, N. Suaud, M. Rapacioli, and F. Spiegelman, An extended DFTB-CI model for charge-transfer excited states in cationic molecular clusters: model studies versus ab initio calculations in small PAH clusters, Physical Chemistry Chemical Physics, vol.18, issue.5, pp.3545-3557, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01270665

L. Dontot, F. Spiegelman, and M. Rapacioli, Structures and Energetics of Neutral and Cationic Pyrene Clusters, The Journal of Physical Chemistry A, vol.123, issue.44, pp.9531-9543, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02385894

D. J. Wales, M. A. Miller, and T. R. Walsh, Archetypal energy landscapes, Nature, vol.394, issue.6695, pp.758-760, 1998.

R. L. Johnston, Evolving better nanoparticles: Genetic algorithms for optimising cluster geometries, Dalton Transactions, vol.22, issue.22, p.4193, 2003.

P. Bobadova-parvanova, K. A. Jackson, S. Srinivas, M. Horoi, C. Köhler et al., Scanning the potential energy surface of iron clusters: A novel search strategy, The Journal of Chemical Physics, vol.116, issue.9, pp.3576-3587, 2002.

C. Köhler, G. Seifert, and T. Frauenheim, Density functional based calculations for Fen (n?32), Chemical Physics, vol.309, issue.1, pp.23-31, 2005.

H. Shi, P. Koskinen, and A. Ramasubramaniam, Self-Consistent Charge Density-Functional Tight-Binding Parametrization for Pt?Ru Alloys, The Journal of Physical Chemistry A, vol.121, issue.12, pp.2497-2502, 2017.

L. J. Wu, L. Zhang, and Y. Qi, Structures and Electronic Properties of a Si₅₅ Cluster on DFTB Calculations, Materials Science Forum, vol.815, pp.49-53, 2015.

Y. Dong and M. Springborg, Unbiased Determination of Structural and Electronic Properties of Gold Clusters with up to 58 Atoms, The Journal of Physical Chemistry C, vol.111, issue.34, pp.12528-12535, 2007.

D. Selli, G. Fazio, and C. Di-valentin, Modelling realistic TiO2 nanospheres: A benchmark study of SCC-DFTB against hybrid DFT, The Journal of Chemical Physics, vol.147, issue.16, p.164701, 2017.

Z. Li and H. A. Scheraga, Monte Carlo-minimization approach to the multiple-minima problem in protein folding., Proceedings of the National Academy of Sciences, vol.84, issue.19, pp.6611-6615, 1987.

D. J. Wales and J. P. Doye, Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms, The Journal of Physical Chemistry A, vol.101, issue.28, pp.5111-5116, 1997.

A. Aktürk and A. Sebetci, BH-DFTB/DFT calculations for iron clusters, AIP Advances, vol.6, issue.5, p.055103, 2016.

T. H. Choi, R. Liang, C. M. Maupin, and G. A. Voth, Application of the SCC-DFTB Method to Hydroxide Water Clusters and Aqueous Hydroxide Solutions, The Journal of Physical Chemistry B, vol.117, issue.17, pp.5165-5179, 2013.

T. H. Choi, Simulation of the (H2O)8 cluster with the SCC-DFTB electronic structure method, Chemical Physics Letters, vol.543, pp.45-49, 2012.

T. W. Yen and S. K. Lai, Use of density functional theory method to calculate structures of neutral carbon clusters Cn (3 ? n ? 24) and study their variability of structural forms, The Journal of Chemical Physics, vol.142, issue.8, p.084313, 2015.

T. Yen, T. Lim, T. Yoon, and S. K. Lai, Studying the varied shapes of gold clusters by an elegant optimization algorithm that hybridizes the density functional tight-binding theory and the density functional theory, Computer Physics Communications, vol.220, pp.143-149, 2017.

X. Chen, Y. Zhao, L. Wang, and J. Li, Recent progresses of global minimum searches of nanoclusters with a constrained Basin-Hopping algorithm in the TGMin program, Computational and Theoretical Chemistry, vol.1107, pp.57-65, 2017.

Y. Zhao, M. Meot-ner-(mautner), and C. Gonzalez, Ionic Hydrogen-Bond Networks and Ion Solvation. 1. An Efficient Monte Carlo/Quantum Mechanical Method for Structural Search and Energy Computations: Ammonium/Water, The Journal of Physical Chemistry A, vol.113, issue.12, pp.2967-2974, 2009.

D. J. Earl and M. W. Deem, Parallel tempering: Theory, applications, and new perspectives, Physical Chemistry Chemical Physics, vol.7, issue.23, p.3910, 2005.

R. H. Swendsen and J. Wang, Replica Monte Carlo Simulation of Spin-Glasses, Physical Review Letters, vol.57, issue.21, pp.2607-2609, 1986.

Y. Sugita and Y. Okamoto, Replica-exchange molecular dynamics method for protein folding, Chemical Physics Letters, vol.314, issue.1-2, pp.141-151, 1999.

Y. Sugita and Y. Okamoto, Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape, Chemical Physics Letters, vol.329, issue.3-4, pp.261-270, 2000.

L. F. Oliveira, N. Tarrat, J. Cuny, J. Morillo, D. Lemoine et al., Benchmarking Density Functional Based Tight-Binding for Silver and Gold Materials: From Small Clusters to Bulk, The Journal of Physical Chemistry A, vol.120, issue.42, pp.8469-8483, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01392312

N. Tarrat, M. Rapacioli, J. Cuny, J. Morillo, J. Heully et al., Global optimization of neutral and charged 20- and 55-atom silver and gold clusters at the DFTB level, Computational and Theoretical Chemistry, vol.1107, pp.102-114, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01529346

K. A. Korchagina, A. Simon, M. Rapacioli, F. Spiegelman, and J. Cuny, Structural Characterization of Sulfur-Containing Water Clusters Using a Density-Functional Based Tight-Binding Approach, The Journal of Physical Chemistry A, vol.120, issue.45, pp.9089-9100, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01418247

K. Korchagina, A. Simon, M. Rapacioli, F. Spiegelman, J. L?hermite et al., Theoretical investigation of the solid?liquid phase transition in protonated water clusters, Phys. Chem. Chem. Phys., vol.19, issue.40, pp.27288-27298, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01620074

M. Rapacioli, R. Barthel, T. Heine, and G. Seifert, Car-Parrinello treatment for an approximate density-functional theory method, The Journal of Chemical Physics, vol.126, issue.12, p.124103, 2007.

M. Rapacioli, A. Simon, C. C. Marshall, J. Cuny, D. Kokkin et al., Cationic Methylene?Pyrene Isomers and Isomerization Pathways: Finite Temperature Theoretical Studies, The Journal of Physical Chemistry A, vol.119, issue.51, pp.12845-12854, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01252811

J. Cuny, K. Korchagina, C. Menakbi, and T. Mineva, Metadynamics combined with auxiliary density functional and density functional tight-binding methods: alanine dipeptide as a case study, Journal of Molecular Modeling, vol.23, issue.3, p.72, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01510587

I. Mitchell, B. Aradi, and A. J. Page, Density functional tight binding-based free energy simulations in the DFTB+ program, Journal of Computational Chemistry, vol.39, issue.29, pp.2452-2458, 2018.

P. Labastie and R. L. Whetten, Statistical thermodynamics of the cluster solid-liquid transition, Physical Review Letters, vol.65, issue.13, pp.1567-1570, 1990.

L. F. Oliveira, J. Cuny, M. Morinière, L. Dontot, A. Simon et al., Phase changes of the water hexamer and octamer in the gas phase and adsorbed on polycyclic aromatic hydrocarbons, Physical Chemistry Chemical Physics, vol.17, issue.26, pp.17079-17089, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01169312

D. A. Mcquarrie, Statistical Mechanics, Harper and, 1976.

A. Candian and C. J. Mackie, Anharmonic interstellar PAH molecules, International Journal of Quantum Chemistry, vol.117, issue.2, pp.146-150, 2016.

G. Mulas, C. Falvo, P. Cassam-chenaï, and C. Joblin, Anharmonic vibrational spectroscopy of polycyclic aromatic hydrocarbons (PAHs), The Journal of Chemical Physics, vol.149, issue.14, p.144102, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01890989

A. Gamboa, M. Rapacioli, and F. Spiegelman, Automatic Differentiation of the Energy within Self-consistent Tight-Binding Methods, Journal of Chemical Theory and Computation, vol.9, issue.9, pp.3900-3907, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00868882

H. A. Witek, S. Irle, and K. Morokuma, Analytical second-order geometrical derivatives of energy for the self-consistent-charge density-functional tight-binding method, The Journal of Chemical Physics, vol.121, issue.11, pp.5163-5170, 2004.

F. Furche and R. Ahlrichs, Erratum: ?Time-dependent density functional methods for excited state properties? [J. Chem. Phys. 117, 7433 (2002)], The Journal of Chemical Physics, vol.121, issue.24, p.12772, 2004.

F. Furche and R. Ahlrichs, Erratum: ?Time-dependent density functional methods for excited state properties? [J. Chem. Phys. 117, 7433 (2002)], The Journal of Chemical Physics, vol.121, issue.24, p.12772, 2004.

D. Heringer, T. A. Niehaus, M. Wanko, and T. Frauenheim, Analytical excited state forces for the time-dependent density-functional tight-binding method, Journal of Computational Chemistry, vol.28, issue.16, pp.2589-2601, 2007.

D. Heringer, T. A. Niehaus, M. Wanko, and T. H. Frauenheim, Analytical excited state forces for the time-dependent density-functional tight-binding method [J. Comp. Chem. 28, 2589], Journal of Computational Chemistry, vol.33, issue.5, pp.593-593, 2011.

T. A. Niehaus, D. Heringer, B. Torralva, and T. H. Frauenheim, Importance of electronic self-consistency in the TDDFT based treatment of nonadiabatic molecular dynamics, The European Physical Journal D, vol.35, issue.3, pp.467-477, 2005.

J. Jakowski and K. Morokuma, Liouville?von Neumann molecular dynamics, The Journal of Chemical Physics, vol.130, issue.22, p.224106, 2009.

Y. Wang, C. Yam, T. H. Frauenheim, G. H. Chen, and T. A. Niehaus, An efficient method for quantum transport simulations in the time domain, Chemical Physics, vol.391, issue.1, pp.69-77, 2011.

C. Oppenländer, B. Korff, T. Frauenheim, and T. A. Niehaus, Atomistic modeling of dynamical quantum transport, physica status solidi (b), vol.250, issue.11, pp.2349-2354, 2013.

J. C. Tully, Molecular dynamics with electronic transitions, The Journal of Chemical Physics, vol.93, issue.2, pp.1061-1071, 1990.

S. Hammes?schiffer and J. C. Tully, Proton transfer in solution: Molecular dynamics with quantum transitions, The Journal of Chemical Physics, vol.101, issue.6, pp.4657-4667, 1994.

R. Mitri?, U. Werner, M. Wohlgemuth, G. Seifert, and V. Bona?i?-koutecký, J. Phys. Chem. A, vol.113, pp.12700-12705, 2009.

E. Tapavicza, I. Tavernelli, and U. Rothlisberger, Trajectory Surface Hopping within Linear Response Time-Dependent Density-Functional Theory, Physical Review Letters, vol.98, issue.2, p.23001, 2007.

E. Tapavicza, I. Tavernelli, U. Rothlisberger, C. Filippi, and M. E. Casida, Mixed time-dependent density-functional theory/classical trajectory surface hopping study of oxirane photochemistry, The Journal of Chemical Physics, vol.129, issue.12, p.124108, 2008.

A. Humeniuk and R. Mitri?, DFTBaby: A software package for non-adiabatic molecular dynamics simulations based on long-range corrected tight-binding TD-DFT(B), Computer Physics Communications, vol.221, pp.174-202, 2017.

L. Stojanovi?, S. G. Aziz, R. H. Hilal, F. Plasser, T. A. Niehaus et al., Nonadiabatic Dynamics of Cycloparaphenylenes with TD-DFTB Surface Hopping, Journal of Chemical Theory and Computation, vol.13, issue.12, pp.5846-5860, 2017.

S. Pal, D. J. Trivedi, A. V. Akimov, B. Aradi, T. Frauenheim et al., Nonadiabatic Molecular Dynamics for Thousand Atom Systems: A Tight-Binding Approach toward PYXAID, Journal of Chemical Theory and Computation, vol.12, issue.4, pp.1436-1448, 2016.

E. Posenitskiy, M. Rapacioli, B. Lepetit, D. Lemoine, and F. Spiegelman, Non-adiabatic molecular dynamics investigation of the size dependence of the electronic relaxation in polyacenes, Physical Chemistry Chemical Physics, vol.21, issue.23, pp.12139-12149, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02156273

T. Krüger, M. Elstner, P. Schiffels, and T. Frauenheim, Validation of the density-functional based tight-binding approximation method for the calculation of reaction energies and other data, The Journal of Chemical Physics, vol.122, issue.11, p.114110, 2005.

G. Zheng, H. A. Witek, P. Bobadova-parvanova, S. Irle, D. G. Musaev et al., Parameter Calibration of Transition-Metal Elements for the Spin-Polarized Self-Consistent-Charge Density-Functional Tight-Binding (DFTB) Method: Sc, Ti, Fe, Co, and Ni, Journal of Chemical Theory and Computation, vol.3, issue.4, pp.1349-1367, 2007.

V. Q. Vuong, J. Akkarapattiakal-kuriappan, M. Kubillus, J. J. Kranz, T. Mast et al., Parametrization and Benchmark of Long-Range Corrected DFTB2 for Organic Molecules, Journal of Chemical Theory and Computation, vol.14, issue.1, pp.115-125, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02289867

M. Gaus, Q. Cui, and M. Elstner, Density functional tight binding: application to organic and biological molecules, Wiley Interdisciplinary Reviews: Computational Molecular Science, vol.4, issue.1, pp.49-61, 2013.

M. Gaus, H. Jin, D. Demapan, A. S. Christensen, P. Goyal et al., DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters, Journal of Chemical Theory and Computation, vol.11, issue.9, pp.4205-4219, 2015.

X. Lu, M. Gaus, M. Elstner, and Q. Cui, Parametrization of DFTB3/3OB for Magnesium and Zinc for Chemical and Biological Applications, The Journal of Physical Chemistry B, vol.119, issue.3, pp.1062-1082, 2014.

A. Simon, M. Rapacioli, M. Lanza, B. Joalland, and F. Spiegelman, Molecular dynamics simulations on [FePAH]+?-complexes of astrophysical interest: anharmonic infrared spectroscopy, Physical Chemistry Chemical Physics, vol.13, issue.8, p.3359, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00843048

T. Kuba?, Z. Bodrog, M. Gaus, C. Köhler, B. Aradi et al., Parametrization of the SCC-DFTB Method for Halogens, Journal of Chemical Theory and Computation, vol.9, issue.7, pp.2939-2949, 2013.

M. Kubillus, T. Kuba?, M. Gaus, J. ?ezá?, and M. Elstner, Parameterization of the DFTB3 Method for Br, Ca, Cl, F, I, K, and Na in Organic and Biological Systems, Journal of Chemical Theory and Computation, vol.11, issue.1, pp.332-342, 2014.

A. A. Darghouth, M. E. Casida, W. Taouali, K. Alimi, M. P. Ljungberg et al., Assessment of Density-Functional Tight-Binding Ionization Potentials and Electron Affinities of Molecules of Interest for Organic Solar Cells Against First-Principles GW Calculations, Computation, vol.3, issue.4, pp.616-656, 2015.

M. Gruden, L. Andjeklovi?, A. K. Jissy, S. Stepanovi?, M. Zlatar et al., Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules, Journal of Computational Chemistry, vol.38, issue.25, pp.2171-2185, 2017.

R. Perriot, C. F. Negre, S. D. Mcgrane, and M. J. Cawkwell, Density functional tight binding calculations for the simulation of shocked nitromethane with LATTE-LAMMPS, AIP Conference Proceedings, p.50014, 2018.

K. H. Lee, U. Schnupf, B. G. Sumpter, and S. Irle, Performance of Density-Functional Tight-Binding in Comparison to Ab Initio and First-Principles Methods for Isomer Geometries and Energies of Glucose Epimers in Vacuo and Solution, ACS Omega, vol.3, issue.12, pp.16899-16915, 2018.

G. Zheng, S. Irle, and K. Morokuma, Performance of the DFTB method in comparison to DFT and semiempirical methods for geometries and energies of C20?C86 fullerene isomers, Chemical Physics Letters, vol.412, issue.1-3, pp.210-216, 2005.

H. A. Witek, S. Irle, G. Zheng, W. A. De-jong, and K. Morokuma, Modeling carbon nanostructures with the self-consistent charge density-functional tight-binding method: Vibrational spectra and electronic structure of C28, C60, and C70, The Journal of Chemical Physics, vol.125, issue.21, p.214706, 2006.

E. Ma?olepsza, H. A. Witek, and S. Irle, Comparison of Geometric, Electronic, and Vibrational Properties for Isomers of Small Fullerenes C20?C36?, The Journal of Physical Chemistry A, vol.111, issue.29, pp.6649-6657, 2007.

E. Ma?olepsza, Y. Lee, H. A. Witek, S. Irle, C. Lin et al., Comparison of geometric, electronic, and vibrational properties for all pentagon/hexagon-bearing isomers of fullerenes C38, C40, and C42, International Journal of Quantum Chemistry, vol.109, issue.9, pp.1999-2011, 2009.

H. Tokoyama, H. Yamakado, S. Maeda, and K. Ohno, Exploration of Isomers of Benzene by GRRM/SCC-DFTB, Chemistry Letters, vol.43, issue.5, pp.702-704, 2014.

C. Dubosq, C. Falvo, F. Calvo, M. Rapacioli, P. Parneix et al., Mapping the structural diversity of C60 carbon clusters and their infrared spectra, Astronomy & Astrophysics, vol.625, p.L11, 2019.

M. Elstner, T. H. Frauenheim, E. Kaxiras, G. Seifert, and S. Suhai, A Self-Consistent Charge Density-Functional Based Tight-Binding Scheme for Large Biomolecules, physica status solidi (b), vol.217, issue.1, pp.357-376, 2000.

S. Eynollahi, S. Riahi, M. R. Ganjali, and P. Norouzi, Int. J. Electrochem. Sci, p.12, 2010.

S. Riahi, S. Eynollahi, and M. R. Ganjali, Computational Studies on Effects of MDMA as an Anticancer Drug on DNA, Chemical Biology & Drug Design, vol.76, issue.5, pp.425-432, 2010.

S. Riahi, S. Eynollahi, and M. R. Ganjali, INTERACTION OF EMODIN WITH DNA BASES: A DENSITY FUNCTIONAL THEORY, Journal of Theoretical and Computational Chemistry, vol.09, issue.05, pp.875-888, 2010.

M. Chehelamirani, M. C. Da-silva, and D. R. Salahub, Electronic properties of carbon nanotubes complexed with a DNA nucleotide, Physical Chemistry Chemical Physics, vol.19, issue.10, pp.7333-7342, 2017.

R. Gutiérrez, R. Caetano, P. B. Woiczikowski, T. Kubar, M. Elstner et al., Structural fluctuations and quantum transport through DNA molecular wires: a combined molecular dynamics and model Hamiltonian approach, New Journal of Physics, vol.12, issue.2, p.023022, 2010.

M. Huang, T. J. Giese, T. Lee, and D. M. York, Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods, Journal of Chemical Theory and Computation, vol.10, issue.4, pp.1538-1545, 2014.

B. M. Sattelle and A. Almond, Assigning kinetic 3D-signatures to glycocodes, Physical Chemistry Chemical Physics, vol.14, issue.16, p.5843, 2012.

Q. Cui and M. Elstner, Density functional tight binding: values of semi-empirical methods in an ab initio era, Phys. Chem. Chem. Phys., vol.16, issue.28, pp.14368-14377, 2014.

M. Elstner, T. Frauenheim, and S. Suhai, An approximate DFT method for QM/MM simulations of biological structures and processes, Journal of Molecular Structure: THEOCHEM, vol.632, issue.1-3, pp.29-41, 2003.

P. Phatak, N. Ghosh, H. Yu, Q. Cui, and M. Elstner, Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin, Proceedings of the National Academy of Sciences, vol.105, issue.50, pp.19672-19677, 2008.

H. Guo and H. Guo, Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity, Proceedings of the National Academy of Sciences, vol.104, issue.21, pp.8797-8802, 2007.

D. Xu and H. Guo, Quantum Mechanical/Molecular Mechanical and Density Functional Theory Studies of a Prototypical Zinc Peptidase (Carboxypeptidase A) Suggest a General Acid?General Base Mechanism, Journal of the American Chemical Society, vol.131, issue.28, pp.9780-9788, 2009.

A. Lodola, D. Branduardi, M. De-vivo, L. Capoferri, M. Mor et al., A Catalytic Mechanism for Cysteine N-Terminal Nucleophile Hydrolases, as Revealed by Free Energy Simulations, PLoS ONE, vol.7, issue.2, p.e32397, 2012.

P. Lian, H. Guo, J. C. Smith, D. Wei, and H. Guo, Catalytic mechanism and origin of high activity of cellulase TmCel12A at high temperature: a quantum mechanical/molecular mechanical study, Cellulose, vol.21, issue.2, pp.937-949, 2013.

I. L. Rogers and K. J. Naidoo, Producing DFT/MM enzyme reaction trajectories from SCC-DFTB/MM driving forces to probe the underlying electronics of a glycosyltransferase reaction, Journal of Computational Chemistry, vol.38, issue.20, pp.1789-1798, 2017.

J. R. Silva, T. Govender, G. E. Maguire, H. G. Kruger, J. Lameira et al., Simulating the inhibition reaction of Mycobacterium tuberculosisl,d-transpeptidase 2 by carbapenems, Chemical Communications, vol.51, issue.63, pp.12560-12562, 2015.

N. Gillet, M. Elstner, and T. Kuba?, Coupled-perturbed DFTB-QM/MM metadynamics: Application to proton-coupled electron transfer, The Journal of Chemical Physics, vol.149, issue.7, p.072328, 2018.

J. Yao, H. Guo, M. Chaiprasongsuk, N. Zhao, F. Chen et al., Substrate-Assisted Catalysis in the Reaction Catalyzed by Salicylic Acid Binding Protein 2 (SABP2), a Potential Mechanism of Substrate Discrimination for Some Promiscuous Enzymes, Biochemistry, vol.54, issue.34, pp.5366-5375, 2015.

H. R. Zhekova, V. Ngo, M. C. Da-silva, D. Salahub, and S. Noskov, Selective ion binding and transport by membrane proteins ? A computational perspective, Coordination Chemistry Reviews, vol.345, pp.108-136, 2017.

S. Wolf, E. Freier, and K. Gerwert, A Delocalized Proton-Binding Site within a Membrane Protein, Biophysical Journal, vol.107, issue.1, pp.174-184, 2014.

D. Riccardi, P. Schaefer, and Q. Cui, pKaCalculations in Solution and Proteins with QM/MM Free Energy Perturbation Simulations: A Quantitative Test of QM/MM Protocols, The Journal of Physical Chemistry B, vol.109, issue.37, pp.17715-17733, 2005.

H. Guo, A. Wlodawer, and H. Guo, A General Acid?Base Mechanism for the Stabilization of a Tetrahedral Adduct in a Serine?Carboxyl Peptidase: A Computational Study, Journal of the American Chemical Society, vol.127, issue.45, pp.15662-15663, 2005.

K. Xiao, X. Wang, and H. Yu, Sci. Rep, vol.9, pp.2045-2322, 2019.

X. Wang, R. Li, W. Cui, Q. Li, and J. Yao, Sci. Rep, vol.8, p.7042, 2018.

A. M. Kulakova, M. G. Khrenova, and A. V. Nemukhin, Simulation of Spectra of Red Fluorescent Protein Mutants, Moscow University Chemistry Bulletin, vol.73, issue.5, pp.212-215, 2018.

A. Bende and I. Turcu, Nitrogen Substituted Phenothiazine Derivatives: Modelling of Molecular Self-Assembling, International Journal of Molecular Sciences, vol.12, issue.5, pp.3102-3116, 2011.

A. Bogaerts, N. Khosravian, J. Van-der-paal, C. C. Verlackt, M. Yusupov et al., Multi-level molecular modelling for plasma medicine, Journal of Physics D: Applied Physics, vol.49, issue.5, p.054002, 2015.

Y. Nishimoto and D. G. Fedorov, The fragment molecular orbital method combined with density-functional tight-binding and the polarizable continuum model, Physical Chemistry Chemical Physics, vol.18, issue.32, pp.22047-22061, 2016.

V. Q. Vuong, Y. Nishimoto, D. G. Fedorov, B. G. Sumpter, T. A. Niehaus et al., The Fragment Molecular Orbital Method Based on Long-Range Corrected Density-Functional Tight-Binding, Journal of Chemical Theory and Computation, vol.15, issue.5, pp.3008-3020, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02364818

V. Tevekeliyska, Y. Dong, M. Springborg, and V. G. Grigoryan, Structural and energetic properties of sodium clusters, The European Physical Journal D, vol.43, issue.1-3, pp.19-22, 2007.

J. Kullgren, M. J. Wolf, K. Hermansson, C. Köhler, B. Aradi et al., Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) Parameters for Ceria in 0D to 3D, The Journal of Physical Chemistry C, vol.121, issue.8, pp.4593-4607, 2017.

J. Frenzel, J. Joswig, and G. Seifert, Optical Excitations in Cadmium Sulfide Nanoparticles, The Journal of Physical Chemistry C, vol.111, issue.29, pp.10761-10770, 2007.

J. Joswig, M. Springborg, and G. Seifert, Structural and Electronic Properties of Cadmium Sulfide Clusters, The Journal of Physical Chemistry B, vol.104, issue.12, pp.2617-2622, 2000.

I. S. Popov, A. N. Enyashin, and A. A. Rempel, Size dependent content of structural vacancies within TiO nanoparticles: Quantum-chemical DFTB study, Superlattices and Microstructures, vol.113, pp.459-465, 2018.

V. C. Fuertes, C. F. Negre, M. B. Oviedo, F. P. Bonafé, F. Y. Oliva et al., A theoretical study of the optical properties of nanostructured TiO2, Journal of Physics: Condensed Matter, vol.25, issue.11, p.115304, 2013.

J. Cuny, N. Tarrat, F. Spiegelman, A. Huguenot, and M. Rapacioli, Density-functional tight-binding approach for metal clusters, nanoparticles, surfaces and bulk: application to silver and gold, Journal of Physics: Condensed Matter, vol.30, issue.30, p.303001, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01847474

P. Koskinen, H. Häkkinen, G. Seifert, S. Sanna, T. Frauenheim et al., Density-functional based tight-binding study of small gold clusters, New Journal of Physics, vol.8, pp.9-9, 2006.

A. Fihey, C. Hettich, J. Touzeau, F. Maurel, A. Perrier et al., SCC-DFTB parameters for simulating hybrid gold-thiolates compounds, Journal of Computational Chemistry, vol.36, issue.27, pp.2075-2087, 2015.

M. Van-den-bossche, H. Grönbeck, and B. Hammer, Tight-Binding Approximation-Enhanced Global Optimization, Journal of Chemical Theory and Computation, vol.14, issue.5, pp.2797-2807, 2018.

P. Koskinen and T. Korhonen, Plenty of motion at the bottom: atomically thin liquid gold membrane, Nanoscale, vol.7, issue.22, pp.10140-10145, 2015.

N. Tarrat, M. Rapacioli, and F. Spiegelman, Au147 nanoparticles: Ordered or amorphous?, The Journal of Chemical Physics, vol.148, issue.20, p.204308, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01806660

N. V. Minh, V. N. Tuoc, and L. T. Lien, Density Functional Based Tight Binding Study on Wurtzite ZnO Prismatic Nanoparticles, Communications in Physics, vol.21, issue.3, p.235, 2011.

A. Enyashin, S. Gemming, and G. Seifert, Nanosized allotropes of molybdenum disulfide, The European Physical Journal Special Topics, vol.149, issue.1, pp.103-125, 2007.

C. Köhler and T. Frauenheim, Magnetic Moment of Iron Clusters with 109, 110, 111, and 147 Atoms, Journal of Computational and Theoretical Nanoscience, vol.4, issue.2, pp.264-269, 2007.

T. Yuan and K. Larsson, Theoretical Study of Size Effects on Surface Chemical Properties for Nanoscale Diamond Particles, The Journal of Physical Chemistry C, vol.118, issue.45, pp.26061-26069, 2014.

W. Li, S. Irle, and H. A. Witek, Convergence in the Evolution of Nanodiamond Raman Spectra with Particle Size: A Theoretical Investigation, ACS Nano, vol.4, issue.8, pp.4475-4486, 2010.

L. Rincon, A. Hasmy, M. Marquez, and C. Gonzalez, A perturbatively corrected tight-binding method with hybridization: Application to gold nanoparticles, Chemical Physics Letters, vol.503, issue.1-3, pp.171-175, 2011.

D. Schebarchov, F. Baletto, and D. J. Wales, Structure, thermodynamics, and rearrangement mechanisms in gold clusters?insights from the energy landscapes framework, Nanoscale, vol.10, issue.4, pp.2004-2016, 2018.

B. Sun, M. Fernandez, and A. S. Barnard, Machine Learning for Silver Nanoparticle Electron Transfer Property Prediction, Journal of Chemical Information and Modeling, vol.57, issue.10, pp.2413-2423, 2017.

A. Simon and F. Spiegelman, Water clusters adsorbed on polycyclic aromatic hydrocarbons: Energetics and conformational dynamics, The Journal of Chemical Physics, vol.138, issue.19, p.194309, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00843526

A. Simon and F. Spiegelman, Conformational dynamics and finite-temperature infrared spectra of the water octamer adsorbed on coronene, Computational and Theoretical Chemistry, vol.1021, pp.54-61, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00868873

A. Simon, M. Rapacioli, J. Mascetti, and F. Spiegelman, Vibrational spectroscopy and molecular dynamics of water monomers and dimers adsorbed on polycyclic aromatic hydrocarbons, Physical Chemistry Chemical Physics, vol.14, issue.19, p.6771, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00843516

C. Pérez, A. L. Steber, A. M. Rijs, B. Temelso, G. C. Shields et al., Corannulene and its complex with water: a tiny cup of water, Physical Chemistry Chemical Physics, vol.19, issue.22, pp.14214-14223, 2017.

P. Goyal, M. Elstner, and Q. Cui, Application of the SCC-DFTB Method to Neutral and Protonated Water Clusters and Bulk Water, The Journal of Physical Chemistry B, vol.115, issue.20, pp.6790-6805, 2011.

C. Wu, C. Lin, H. Chang, J. Jiang, J. Kuo et al., Protonated clathrate cages enclosing neutral water molecules: H+(H2O)21 and H+(H2O)28, The Journal of Chemical Physics, vol.122, issue.7, p.074315, 2005.

S. S. Iyengar, M. K. Petersen, T. J. Day, C. J. Burnham, V. E. Teige et al., The properties of ion-water clusters. I. The protonated 21-water cluster, The Journal of Chemical Physics, vol.123, issue.8, p.084309, 2005.

H. Yu and Q. Cui, The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding, The Journal of Chemical Physics, vol.127, issue.23, p.234504, 2007.

L. Dontot, F. Spiegelman, and M. Rapacioli, Structures and Energetics of Neutral and Cationic Pyrene Clusters, The Journal of Physical Chemistry A, vol.123, issue.44, pp.9531-9543, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02385894

S. Zamith, M. Ji, J. L?hermite, C. Joblin, L. Dontot et al., Thermal evaporation of pyrene clusters, The Journal of Chemical Physics, vol.151, issue.19, p.194303, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02375800

J. Bernard, A. Al-mogeeth, L. Dontot, S. Martin, C. Joblin et al.,

G. Garcia, L. Nahon, L. Dontot, F. Spiegelman, M. Rapacioli et al.,

C. Joblin, L. Dontot, G. A. Garcia, F. Spiegelman, M. Rapacioli et al., Size Effect in the Ionization Energy of PAH Clusters, The Journal of Physical Chemistry Letters, vol.8, issue.15, pp.3697-3702, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01583599

M. A. Addicoat, S. Fukuoka, A. J. Page, and S. Irle, Stochastic structure determination for conformationally flexible heterogenous molecular clusters: Application to ionic liquids, Journal of Computational Chemistry, vol.34, issue.30, pp.2591-2600, 2013.

M. A. Addicoat, R. Stefanovic, G. B. Webber, R. Atkin, and A. J. Page, Assessment of the Density Functional Tight Binding Method for Protic Ionic Liquids, Journal of Chemical Theory and Computation, vol.10, issue.10, pp.4633-4643, 2014.

N. H. Moreira, G. Dolgonos, B. Aradi, A. L. Da-rosa, and T. Frauenheim, Toward an Accurate Density-Functional Tight-Binding Description of Zinc-Containing Compounds, Journal of Chemical Theory and Computation, vol.5, issue.3, pp.605-614, 2009.

W. Li, K. Kotsis, and S. Manzhos, Comparative density functional theory and density functional tight binding study of arginine and arginine-rich cell penetrating peptide TAT adsorption on anatase TiO2, Physical Chemistry Chemical Physics, vol.18, issue.29, pp.19902-19917, 2016.

V. Mäkinen, P. Koskinen, and H. Häkkinen, Modeling thiolate-protected gold clusters with density-functional tight-binding, The European Physical Journal D, vol.67, issue.2, p.38, 2013.

A. Domínguez-castro, D. Hernández, and F. Guzmán, Insights into the interactions of biomolecules with small gold clusters: a theoretical study from a DFTB perspective, Theoretical Chemistry Accounts, vol.136, issue.7, p.84, 2017.

O. A. Douglas-gallardo, M. Berdakin, and C. G. Sánchez, Atomistic Insights into Chemical Interface Damping of Surface Plasmon Excitations in Silver Nanoclusters, The Journal of Physical Chemistry C, vol.120, issue.42, pp.24389-24399, 2016.

F. P. Bonafé, B. Aradi, M. Guan, O. A. Douglas-gallardo, C. Lian et al., Plasmon-driven sub-picosecond breathing of metal nanoparticles, Nanoscale, vol.9, issue.34, pp.12391-12397, 2017.

K. L. Kelly, E. Coronado, L. L. Zhao, and G. C. Schatz, The Optical Properties of Metal Nanoparticles: The Influence of Size, Shape, and Dielectric Environment, The Journal of Physical Chemistry B, vol.107, issue.3, pp.668-677, 2003.

S. Eustis and M. A. El-sayed, Why gold nanoparticles are more precious than pretty gold: Noble metal surface plasmon resonance and its enhancement of the radiative and nonradiative properties of nanocrystals of different shapes, Chem. Soc. Rev., vol.35, issue.3, pp.209-217, 2006.

J. E. Millstone, S. J. Hurst, G. S. Métraux, J. I. Cutler, and C. A. Mirkin, Colloidal Gold and Silver Triangular Nanoprisms, Small, vol.5, issue.6, pp.646-664, 2009.

O. A. Douglas-gallardo, G. J. Soldano, M. M. Mariscal, and C. G. Sánchez, Effects of oxidation on the plasmonic properties of aluminum nanoclusters, Nanoscale, vol.9, issue.44, pp.17471-17480, 2017.

M. B. Oviedo, X. Zarate, C. F. Negre, E. Schott, R. Arratia-pérez et al., Quantum Dynamical Simulations as a Tool for Predicting Photoinjection Mechanisms in Dye-Sensitized TiO2 Solar Cells, The Journal of Physical Chemistry Letters, vol.3, issue.18, pp.2548-2555, 2012.

C. F. Negre, V. C. Fuertes, M. B. Oviedo, F. Y. Oliva, and C. G. Sánchez, Quantum Dynamics of Light-Induced Charge Injection in a Model Dye?Nanoparticle Complex, The Journal of Physical Chemistry C, vol.116, issue.28, pp.14748-14753, 2012.

C. F. Negre, K. J. Young, M. B. Oviedo, L. J. Allen, C. G. Sánchez et al., Photoelectrochemical Hole Injection Revealed in Polyoxotitanate Nanocrystals Functionalized with Organic Adsorbates, Journal of the American Chemical Society, vol.136, issue.46, pp.16420-16429, 2014.

Y. L. Zhao, S. Köppen, and T. Frauenheim, An SCC-DFTB/MD Study of the Adsorption of Zwitterionic Glycine on a Geminal Hydroxylated Silica Surface in an Explicit Water Environment, The Journal of Physical Chemistry C, vol.115, issue.19, pp.9615-9621, 2011.

Y. Zhao, C. Wang, Y. Zhai, R. Zhang, and M. A. Van-hove, Selective adsorption ofl-serine functional groups on the anatase TiO2(101) surface in benthic microbial fuel cells, Phys. Chem. Chem. Phys., vol.16, issue.38, pp.20806-20817, 2014.

S. Manzhos, G. Giorgi, and K. Yamashita, A Density Functional Tight Binding Study of Acetic Acid Adsorption on Crystalline and Amorphous Surfaces of Titania, Molecules, vol.20, issue.2, pp.3371-3388, 2015.

L. Guo, C. Qi, X. Zheng, R. Zhang, X. Shen et al., Toward understanding the adsorption mechanism of large size organic corrosion inhibitors on an Fe(110) surface using the DFTB method, RSC Advances, vol.7, issue.46, pp.29042-29050, 2017.

Y. Kanematsu, K. Gohara, H. Yamada, and Y. Takano, Applicability of Density Functional Tight Binding Method with Dispersion Correction to Investigate the Adsorption of Porphyrin/Porphycene Metal Complexes on Graphene, Chemistry Letters, vol.46, issue.1, pp.51-52, 2017.

D. Li, F. Wang, Z. Zhang, W. Jiang, Y. Zhu et al., The nature of small molecules adsorbed on defective carbon nanotubes, Royal Society Open Science, vol.6, issue.8, p.190727, 2019.

G. Fan, S. Zhu, and H. Xu, Density-functional theory study of the interaction mechanism and optical properties of flavonols on the boron nitride nanotubes, International Journal of Quantum Chemistry, vol.118, issue.7, p.e25514, 2017.

G. Dolgonos, B. Aradi, N. H. Moreira, and T. Frauenheim, An Improved Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) Set of Parameters for Simulation of Bulk and Molecular Systems Involving Titanium, Journal of Chemical Theory and Computation, vol.6, issue.1, pp.266-278, 2009.

N. Goldman, B. Aradi, R. K. Lindsey, and L. E. Fried, Development of a Multicenter Density Functional Tight Binding Model for Plutonium Surface Hydriding, Journal of Chemical Theory and Computation, vol.14, issue.5, pp.2652-2660, 2018.

M. P. Bernstein, S. A. Sandford, A. L. Mattioda, and L. J. Allamandola, Near? and Mid?Infrared Laboratory Spectra of PAH Cations in Solid H2O, The Astrophysical Journal, vol.664, issue.2, pp.1264-1272, 2007.

K. I. Osberg, Chem. Rev, vol.116, pp.9631-9663, 2016.

M. S. Gudipati and L. J. Allamandola, Polycyclic Aromatic Hydrocarbon Ionization Energy Lowering in Water Ices, The Astrophysical Journal, vol.615, issue.2, pp.L177-L180, 2004.

D. E. Woon and J. Y. Park, Photoionization of Benzene and Small Polycyclic Aromatic Hydrocarbons in Ultraviolet?processed Astrophysical Ices: A Computational Study, The Astrophysical Journal, vol.607, issue.1, pp.342-345, 2004.

Z. Guennoun, C. Aupetit, and J. Mascetti, Photochemistry of coronene with water at 10 K: first tentative identification by infrared spectroscopy of oxygen containing coronene products, Physical Chemistry Chemical Physics, vol.13, issue.16, p.7340, 2011.

Z. Guennoun, C. Aupetit, and J. Mascetti, Photochemistry of Pyrene with Water at Low Temperature: Study of Atmospherical and Astrochemical Interest, The Journal of Physical Chemistry A, vol.115, issue.10, pp.1844-1852, 2011.

J. Bouwman, D. M. Paardekooper, H. M. Cuppen, H. Linnartz, and L. J. Allamandola, REAL-TIME OPTICAL SPECTROSCOPY OF VACUUM ULTRAVIOLET IRRADIATED PYRENE:H2O INTERSTELLAR ICE, The Astrophysical Journal, vol.700, issue.1, pp.56-62, 2009.

E. Michoulier, J. A. Noble, A. Simon, J. Mascetti, and C. Toubin, Correction: Adsorption of PAHs on interstellar ice viewed by classical molecular dynamics, Physical Chemistry Chemical Physics, vol.20, issue.16, pp.11483-11483, 2018.

A. Simon, M. Rapacioli, E. Michoulier, L. Zheng, K. Korchagina et al., Contribution of the density-functional-based tight-binding scheme to the description of water clusters: methods, applications and extension to bulk systems, Molecular Simulation, vol.45, issue.4-5, pp.249-268, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01965494

A. Simon, C. Iftner, J. Mascetti, and F. Spiegelman, Water Clusters in an Argon Matrix: Infrared Spectra from Molecular Dynamics Simulations with a Self-Consistent Charge Density Functional-Based Tight Binding/Force-Field Potential, The Journal of Physical Chemistry A, vol.119, issue.11, pp.2449-2467, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01149493

B. Sz?cs, Z. Hajnal, R. Scholz, S. Sanna, and T. Frauenheim, Theoretical study of the adsorption of a PTCDA monolayer on S-passivated GaAs(l00), Applied Surface Science, vol.234, issue.1-4, pp.173-177, 2004.

Y. Chen, M. Liu, J. Chen, Y. Li, C. Zhao et al., A density functional based tight binding (DFTB+) study on the sulfidization-amine flotation mechanism of smithsonite, Applied Surface Science, vol.458, pp.454-463, 2018.

M. Hellström, K. Jorner, M. Bryngelsson, S. E. Huber, J. Kullgren et al., An SCC-DFTB Repulsive Potential for Various ZnO Polymorphs and the ZnO?Water System, The Journal of Physical Chemistry C, vol.117, issue.33, pp.17004-17015, 2013.

D. Selli, G. Fazio, G. Seifert, and C. Di-valentin, Water Multilayers on TiO2 (101) Anatase Surface: Assessment of a DFTB-Based Method, Journal of Chemical Theory and Computation, vol.13, issue.8, pp.3862-3873, 2017.

N. Prasetyo and T. S. Hofer, Adsorption and dissociation of water molecules at the ?-Al2O3(0001) surface: A 2-dimensional hybrid self-consistent charge density functional based tight-binding/molecular mechanics molecular dynamics (2D SCC-DFTB/MM MD) simulation study, Computational Materials Science, vol.164, pp.195-204, 2019.

H. Li, A. J. Page, C. Hettich, B. Aradi, C. Köhler et al., Graphene nucleation on a surface-molten copper catalyst: quantum chemical molecular dynamics simulations, Chem. Sci., vol.5, issue.9, pp.3493-3500, 2014.

S. Abdalla, M. Springborg, and Y. Dong, Isolated and deposited potassium clusters: Energetic and structural properties, Surface Science, vol.608, pp.255-264, 2013.

X. Lin, N. Nilius, M. Sterrer, P. Koskinen, H. Häkkinen et al., Characterizing low-coordinated atoms at the periphery of MgO-supported Au islands using scanning tunneling microscopy and electronic structure calculations, Physical Review B, vol.81, issue.15, p.153406, 2010.

C. Stiehler, Y. Pan, W. Schneider, P. Koskinen, H. Häkkinen et al., Electron quantization in arbitrarily shaped gold islands on MgO thin films, Physical Review B, vol.88, issue.11, p.115415, 2013.

H. A. Witek, K. Morokuma, and A. Stradomska, MODELING VIBRATIONAL SPECTRA USING THE SELF-CONSISTENT CHARGE DENSITY-FUNCTIONAL TIGHT-BINDING METHOD II: INFRARED SPECTRA, Journal of Theoretical and Computational Chemistry, vol.04, issue.spec01, pp.639-655, 2005.

H. A. Witek, K. Morokuma, and A. Stradomska, Modeling vibrational spectra using the self-consistent charge density-functional tight-binding method. I. Raman spectra, The Journal of Chemical Physics, vol.121, issue.11, pp.5171-5178, 2004.

H. A. Witek and K. Morokuma, Systematic study of vibrational frequencies calculated with the self-consistent charge density functional tight-binding method, Journal of Computational Chemistry, vol.25, issue.15, pp.1858-1864, 2004.

A. J. Page, C. Chou, B. Q. Pham, H. A. Witek, S. Irle et al., Quantum chemical investigation of epoxide and ether groups in graphene oxide and their vibrational spectra, Physical Chemistry Chemical Physics, vol.15, issue.11, p.3725, 2013.

H. F. Santos, L. A. Souza, W. B. De-almeida, and T. Heine, J. Phys. Chem. C, vol.118, pp.24761-24768, 2014.

S. Kaminski, M. Gaus, P. Phatak, D. Von-stetten, M. Elstner et al., Vibrational Raman Spectra from the Self-Consistent Charge Density Functional Tight Binding Method via Classical Time-Correlation Functions, Journal of Chemical Theory and Computation, vol.6, issue.4, pp.1240-1255, 2010.

B. Joalland, M. Rapacioli, A. Simon, C. Joblin, C. J. Marsden et al., Molecular Dynamics Simulations of Anharmonic Infrared Spectra of [SiPAH]+?-Complexes, The Journal of Physical Chemistry A, vol.114, issue.18, pp.5846-5854, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00843706

A. Simon, M. Rapacioli, G. Rouaut, G. Trinquier, and F. X. Gadéa, Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol.375, issue.2092, p.20160195, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01493419

F. Pietrucci, Strategies for the exploration of free energy landscapes: Unity in diversity and challenges ahead, Reviews in Physics, vol.2, pp.32-45, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01534581

G. M. Torrie and J. P. Valleau, Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling, Journal of Computational Physics, vol.23, issue.2, pp.187-199, 1977.

A. Laio and M. Parrinello, Escaping free-energy minima, Proceedings of the National Academy of Sciences, vol.99, issue.20, pp.12562-12566, 2002.

M. Rapacioli, S. Cazaux, N. Foley, A. Simon, R. Hoekstra et al., Atomic hydrogen interactions with gas-phase coronene cations: hydrogenation versus fragmentation, Physical Chemistry Chemical Physics, vol.20, issue.35, pp.22427-22438, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01895787

A. Simon, J. P. Champeaux, M. Rapacioli, P. Moretto-capelle, F. X. Gadéa et al., Dissociation of polycyclic aromatic hydrocarbons at high energy: MD/DFTB simulations versus collision experiments, Theoretical Chemistry Accounts, vol.137, issue.7, p.106, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01873276

K. A. Korchagina, F. Spiegelman, and J. Cuny, Molecular Dynamics Study of the Collision-Induced Reaction of H with CO on Small Water Clusters, The Journal of Physical Chemistry A, vol.121, issue.49, pp.9485-9494, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01684045

F. , J. Dominguez-gutierrez, P. S. Krstic, S. Irle, and R. Cabrera-trujillo, Carbon, vol.134, pp.189-198, 2018.

H. Qian, A. C. Van-duin, K. Morokuma, and S. Irle, Reactive Molecular Dynamics Simulation of Fullerene Combustion Synthesis: ReaxFF vs DFTB Potentials, Journal of Chemical Theory and Computation, vol.7, issue.7, pp.2040-2048, 2011.

B. Saha, S. Shindo, S. Irle, and K. Morokuma, Quantum Chemical Molecular Dynamics Simulations of Dynamic Fullerene Self-Assembly in Benzene Combustion, ACS Nano, vol.3, issue.8, pp.2241-2257, 2009.

B. Saha, S. Irle, and K. Morokuma, Formation mechanism of polycyclic aromatic hydrocarbons in benzene combustion: Quantum chemical molecular dynamics simulations, The Journal of Chemical Physics, vol.132, issue.22, p.224303, 2010.

Y. Ohta, Y. Okamoto, S. Irle, and K. Morokuma, Rapid Growth of a Single-Walled Carbon Nanotube on an Iron Cluster: Density-Functional Tight-Binding Molecular Dynamics Simulations, ACS Nano, vol.2, issue.7, pp.1437-1444, 2008.

G. Zheng, S. Irle, and K. Morokuma, Fe/C Interactions During SWNT Growth with C<SUB>2</SUB> Feedstock Molecules: A Quantum Chemical Molecular Dynamics Study, Journal of Nanoscience and Nanotechnology, vol.6, issue.5, pp.1259-1270, 2006.

Z. Wang, S. Irle, G. Zheng, M. Kusunoki, and K. Morokuma, Carbon Nanotubes Grow on the C Face of SiC (0001?) during Sublimation Decomposition: Quantum Chemical Molecular Dynamics Simulations, The Journal of Physical Chemistry C, vol.111, issue.35, pp.12960-12972, 2007.

Q. Deng, T. Heine, S. Irle, and A. A. Popov, Self-assembly of endohedral metallofullerenes: a decisive role of cooling gas and metal?carbon bonding, Nanoscale, vol.8, issue.6, pp.3796-3808, 2016.

W. A. Adeagbo and P. Entel, Determination of melting of water clusters using density functional theory, Phase Transitions, vol.77, issue.1-2, pp.63-79, 2004.

M. Rapacioli, N. Tarrat, and F. Spiegelman, Melting of the Au20Gold Cluster: Does Charge Matter?, The Journal of Physical Chemistry A, vol.122, issue.16, pp.4092-4098, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01779774

M. Rapacioli, N. Tarrat, and F. Spiegelman, Melting of the Au20Gold Cluster: Does Charge Matter?, The Journal of Physical Chemistry A, vol.122, issue.16, pp.4092-4098, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01779774

T. A. Niehaus, M. Meziane, F. Lepine, A. Marciniak, K. Yamazaki et al., Pulse shape and molecular orientation determine the attosecond charge migration in Caffeine, The European Physical Journal B, vol.91, issue.7, p.152, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02290277

E. Titov, A. Humeniuk, and R. Mitri?, Exciton localization in excited-state dynamics of a tetracene trimer: a surface hopping LC-TDDFTB study, Physical Chemistry Chemical Physics, vol.20, issue.40, pp.25995-26007, 2018.

C. R. Medrano, M. B. Oviedo, and C. G. Sánchez, Photoinduced charge-transfer dynamics simulations in noncovalently bonded molecular aggregates, Physical Chemistry Chemical Physics, vol.18, issue.22, pp.14840-14849, 2016.

A. A. Darghouth, G. C. Correa, S. Juillard, M. E. Casida, A. Humeniuk et al., Davydov-type excitonic effects on the absorption spectra of parallel-stacked and herringbone aggregates of pentacene: Time-dependent density-functional theory and time-dependent density-functional tight binding, The Journal of Chemical Physics, vol.149, issue.13, p.134111, 2018.

J. Hoche, H. Schmitt, A. Humeniuk, I. Fischer, R. Mitri? et al., The mechanism of excimer formation: an experimental and theoretical study on the pyrene dimer, Physical Chemistry Chemical Physics, vol.19, issue.36, pp.25002-25015, 2017.

P. Plötz, J. Megow, T. Niehaus, and O. Kühn, All-DFTB Approach to the Parametrization of the System-Bath Hamiltonian Describing Exciton-Vibrational Dynamics of Molecular Assemblies, Journal of Chemical Theory and Computation, vol.14, issue.10, pp.5001-5010, 2018.

P. A. Plötz, S. P. Polyutov, S. D. Ivanov, F. Fennel, S. Wolter et al., Biphasic aggregation of a perylene bisimide dye identified by exciton-vibrational spectra, Physical Chemistry Chemical Physics, vol.18, issue.36, pp.25110-25119, 2016.

C. F. Negre, E. M. Perassi, E. A. Coronado, and C. G. Sánchez, Quantum dynamical simulations of local field enhancement in metal nanoparticles, Journal of Physics: Condensed Matter, vol.25, issue.12, p.125304, 2013.

B. Aradi, B. Hourahine, and T. H. Frauenheim, DFTB+, a Sparse Matrix-Based Implementation of the DFTB Method?, The Journal of Physical Chemistry A, vol.111, issue.26, pp.5678-5684, 2007.

T. Heine, M. Rapacioli, S. Patchkovskii, J. Frenzel, A. Koster et al., , 2009.

G. Velde, F. M. Bickelhaupt, E. J. Baerends, C. Guerra, S. J. Van-gisbergen et al., J. Comput. Chem, vol.22, pp.931-967, 2001.

R. Salomon-ferrer, D. A. Case, and R. C. Walker, An overview of the Amber biomolecular simulation package, Wiley Interdisciplinary Reviews: Computational Molecular Science, vol.3, issue.2, pp.198-210, 2012.

H. J. Berendsen, D. Van-der-spoel, and R. Van-drunen, GROMACS: A message-passing parallel molecular dynamics implementation, Computer Physics Communications, vol.91, issue.1-3, pp.43-56, 1995.

M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb et al., , 2016.

J. Hutter, M. Iannuzzi, F. Schiffmann, and J. Vandevondele, cp2k: atomistic simulations of condensed matter systems, Wiley Interdisciplinary Reviews: Computational Molecular Science, vol.4, issue.1, pp.15-25, 2013.

A. Scemama, N. Renon, and M. Rapacioli, A Sparse Self-Consistent Field Algorithm and Its Parallel Implementation: Application to Density-Functional-Based Tight Binding, Journal of Chemical Theory and Computation, vol.10, issue.6, pp.2344-2354, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00992187

K. Kosugi, H. Nakano, and H. Sato, SCC-DFTB-PIMD Method To Evaluate a Multidimensional Quantum Free-Energy Surface for a Proton-Transfer Reaction, Journal of Chemical Theory and Computation, vol.15, issue.9, pp.4965-4973, 2019.

M. Head?gordon and J. C. Tully, Molecular dynamics with electronic frictions, The Journal of Chemical Physics, vol.103, issue.23, pp.10137-10145, 1995.

T. J. Giese, H. Chen, T. Dissanayake, G. M. Giamba?u, H. Heldenbrand et al., A Variational Linear-Scaling Framework to Build Practical, Efficient Next-Generation Orbital-Based Quantum Force Fields, Journal of Chemical Theory and Computation, vol.9, issue.3, pp.1417-1427, 2013.

H. Zhang, P. Zapol, D. A. Dixon, A. F. Wagner, and M. Keceli, Journal of Computational Chemistry, p.37, 2015.

H. Nishizawa, Y. Nishimura, M. Kobayashi, S. Irle, and H. Nakai, Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation, Journal of Computational Chemistry, vol.37, issue.21, pp.1983-1992, 2016.